How To Tell If Your Gut Is The Cause of Your Health Issues

If you’ve heard about ‘gut health’ and thought that it doesn’t apply to you because you don’t have celiac disease, Ulcerative Colitis, Crohn’s disease, or another inflammatory gut issue, think again. EVERYone should be focused on gut health, as it is the root of all health and disease.

My nutrition clients and readers often indicate that they don’t think they have any issues with gut health because they’re not having digestive issues specifically. In almost every case, it’s not long before we uncover that their health issues and concerns are directly linked to the health of their gut!

Gut health isn’t just about digestion, it’s at the root of all illness and disease.
As Hippocrates famously said 2,000 years ago: “All disease begins in the gut.”

In fact, current research shows that the health of our intestines is responsible for most chronic conditions, from autoimmune disorders and neurological problems, to skin conditions and more! The health of your gut isn’t just about your digestion, it literally impacts every area of health.

If your gut isn’t healthy, it’s hard for you to be healthy!

Some facts about your gut:

  • 80% of your immune system lies within your gut.
  • Your gut impacts your mood and how you think. The gut sends emotional signals to the brain (at least the brain perceives them to be emotional signals). This is because 95% of our serotonin is produced in the gut, which affects our mood, anxiety, depression, etc. Over half of our bodies dopamine is produced in the gut.
  • Your gut microbiome (the microbe population living in your intestines) influences what you eat and how much you eat. Think cravings are just about willpower? (They’re impacted by your gut too!)
  • Environmental toxins (like chlorine & fluoride in drinking water and chemicals we come into contact with) and antibiotics kill off good bacteria in the gut.
  • It can take your gut flora up to one year to fully repopulate itself after just one round of antibiotics (wow!)

The Beginning of My Gut Health Story

Even though growing up on the Standard American Diet certainly took it’s toll on my gut health, it wasn’t until I was on antibiotics for 3-4 years during my teenage years (in the hopes of clearing my skin) that I started to realize my gut health was declining. Not only did these pills NOT work, but they destroyed my gut (literally). It was during and after this time, I noticed my health start to decline – fast. I found myself getting sick much too frequently, and those colds and flus often turned into pneumonia and bronchitis because my immune system was shot from the damage of the antibiotics. I struggled with candida (which I’ll talk about more in Part 2) and it’s side effects (fatigue, brain fog, recurring yeast infections, and more) for years after this.

Focusing on improving gut health has been the single biggest factor in renewing my health, but we’ll talk about that more in Part 2!

Now Here: Gut Health Discovery Sessions

A note about antibiotics (they destroyed my health)

Anti-biotics: think about the root of the word. Antibiotics kill life forms in the body. The problem is that they kill both harmful bacteria AND beneficial bacteria (which we need.)

I realize there are situations in which antibiotics are necessary and important, but for many health issues, safe alternatives can be used which do not bring a host of short-term and long-term side effects along with them.

Many infections are viral, meaning that antibiotics don’t help in the first place, but instead destroy the beneficial bacteria inside our guts (which keep us healthy & well!)

What is gut microflora?

It’s impossible to understand gut health without first understanding gut flora. Gut flora is the complex community of beneficial bacteria and harmful bacteria living inside the gut.

“An estimated 100 trillion microorganisms representing more than 500 different species inhabit every normal, healthy bowel. These microorganisms (or microflora) generally don’t make us sick; most are helpful. Gut-dwelling bacteria keep pathogens (harmful microorganisms) in check, aid digestion and nutrient absorption, and contribute to immune function.” (Source)

Bacteria outnumbers the cells in our bodies by 10-to-1, so we are actually more bacteria than cells! It’s no surprise that gut health is absolutely critical for everyone to focus on.

We all have both beneficial bacteria and harmful bacteria in our guts. The problems arise when the harmful bacteria start to outnumber the beneficial bacteria.

To keep it simple, here’s an analogy: a healthy gut resembles a shag carpet with tall villi that function properly. A damaged gut, on the other hand, resembles a flat carpet. Like this:

gut health

Villi are responsible for the absorption of nutrients, in addition to normal digestion. When villi are damaged, both our digestion and absorption are affected. So, even if you’re eating healthfully most of the time, your body isn’t able to absorb the nutrients you’re consuming (if your gut is damaged).

Factors that Damage Gut Health

  • Antibiotics (even one round of antibiotics!)
  • Over the counter medications and painkillers (NSAIDs)
  • Sugar (sometimes even natural sugar)
  • Chronic Stress
  • Environmental toxins (inhaled, consumed, and applied to the skin)
  • Conventionally raised meats (which contain antibiotics)
  • Processed foods & their additives
  • Antibacterial soap (this can be another article in itself, but antibacterial soaps do MUCH more harm than good. Switch to this safe, nontoxic soap that doesn’t kill beneficial bacteria!)

Signs & Symptoms That Your Gut Needs Attention

Digestive issues (like acid reflux, constipation, diarrhea, bloatedness) are only ONE of the signs that your gut needs some attention! It goes far beyond these types of symptoms.

If you’re experiencing any of the following, it’s likely that your gut microbiome is out of balance…

  • Food Intolerances and Sensitivities
  • Autoimmune Issues (of any kind!)
  • Skin Conditions (acne, eczema, psoriasis, even Keratosis Pilaris and more!)
  • Mental / Cognitive Issues (migraines, brain fog, even autism)
  • A Weak Immune System (find yourself getting sick often?)
  • Obesity, Diabetes, and other chronic metabolic conditions
  • Other chronic health issues (sinusitis, asthma, fibromyalgia, rheumatoid arthritis, etc.)

If you’re ready to get clear about how to heal your gut, you can work with me one-on-one through Gut Health Discovery:

Yes, I'm ready for my gut-healing protocol!

The Connection Between Cesarean Deliveries and Gut Health

Did you know that gut health starts at birth? Vaginal deliveries ‘inoculate’ the baby with the mother’s vaginal and intestinal flora, which is critical in developing a healthy flora for the baby. During cesarean deliveries, this contact is absent, which can have long-term consequences for the child. Children that were delivered via c-section may experience chronic immune conditions, skin conditions, food allergies & intolerances, etc. Check out this article for an interesting perspective on how to promote gut health for your baby if you deliver via c-section.

Do you suspect gut issues could be a cause of your health concerns? Let me know below!


Hannah Smith

Hannah is the founder and health educator at Healthfully Hannah, empowering women to live healthfully through science-based, step-by-step guidance. Read Hannah’s personal health journey that led her to discover the power of Functional Medicine and Nutrition. Feel free to send Hannah a message here.


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  1. Hi Hannah – This is such a helpful and informative blog post! Two years ago I was able to (slowly) take myself off of the anti-anxiety medication I took for almost twenty years. It’s been a tough road to adjusting to life without medication, but worth it and I’m in a good place. I’m seeking natural ways to manage the physical symptoms of my anxiety. Regular exercise, healthy-ish eating, friends and my faith have helped tremendously, but I still have trouble sleeping, experience a racing heartbeat and restlessness. I’ve tried different herbal supplements but the best “relief” I’ve gotten so far is from probiotics! I’m reading a lot about the mind/gut connection and see truth in it based on my experience. I’m looking forward to reading the future blog posts and am interested in learning more about what kind of diet/foods will help restore my gut health. Any info/resources are appreciated!

    1. Hi Andrea, thank you for your comment! I’m so glad to hear this blog post was helpful for you. That is an amazing accomplishment to slowly wean yourself off of the medication. I’m sure it has been a tough adjustment, but you’re right – definitely worth it. Also, I’m glad you’ve experienced such dramatic results from probiotics, that is wonderful news!

      Yes, the gut and mind are so intricately connected (one reason they call the gut our second brain!) I plan to focus on various ways to restore gut health with food & supplements in the next part of this series, so that will be helpful for you. As always, let me know if you think of any additional questions I can help with. 🙂

  2. I just joined your community and I’m so excited. I do believe I have gut issues. I have a gluten sensitivity and often experience heartburn or acid reflux. My husband was just diagnosed with diabetics and we eat pretty good and our Natruopath was surprised at this his blood test results, which I don’t want to ignore. I’d love him to heal naturally. He just started taking conventional medicine and it’s making him sick and this medication is the one with the least side effects

    1. Hi Kim! I’m so excited you’re here 🙂 Those can be signs of gut dysfunction, as you said. I’m glad you’re going to a naturopath too. Healing naturally is often the best way!